AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene060778


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060778.t1 MTR_4g032805 96.774 248 7 1 1 248 23 269 0.0 500
MS.gene060778.t1 MTR_2g097690 50.000 62 29 1 109 170 77 136 3.59e-12 63.9
MS.gene060778.t1 MTR_5g022180 37.500 88 52 2 87 173 53 138 6.56e-12 62.4
MS.gene060778.t1 MTR_2g097690 50.000 64 30 1 107 170 75 136 1.41e-11 63.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060778.t1 AT4G09350 59.389 229 82 3 20 247 28 246 1.73e-96 283
MS.gene060778.t1 AT5G59610 49.231 65 31 1 105 169 71 133 2.58e-11 62.4
MS.gene060778.t1 AT5G59610 49.231 65 31 1 105 169 71 133 6.09e-11 61.6
MS.gene060778.t1 AT5G59610 49.231 65 31 1 105 169 71 133 6.09e-11 61.6
MS.gene060778.t1 AT5G59610 49.231 65 31 1 105 169 71 133 6.81e-11 61.2
MS.gene060778.t1 AT5G59610 49.231 65 31 1 105 169 71 133 6.81e-11 61.2

Find 40 sgRNAs with CRISPR-Local

Find 78 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTTCACCCAAAAGCTTCTT+AGG 0.196506 4.4:-70833533 None:intergenic
CTACTATTCAATCCAATCTT+AGG 0.223430 4.4:+70833299 MS.gene060778:CDS
TCTTATTCTTCTTATTGTTT+TGG 0.269689 4.4:-70833327 None:intergenic
GGAGAAACCTAAGAAGCTTT+TGG 0.298843 4.4:+70833526 MS.gene060778:CDS
AAGCAATCAAAGTAGCTTTC+AGG 0.300211 4.4:+70834275 MS.gene060778:CDS
ATGAAAACAAGCAGATTCTT+AGG 0.302121 4.4:+70834229 MS.gene060778:intron
TGCATTGGTTTGTTGCTGTT+TGG 0.332246 4.4:-70833501 None:intergenic
ATTGCTTCTACATCAGCTTC+TGG 0.336747 4.4:-70834259 None:intergenic
GCAAGTTCATGCTTCTACTA+AGG 0.365942 4.4:+70833391 MS.gene060778:CDS
GAAACTGAAAATAAAATTAG+AGG 0.366458 4.4:+70834462 MS.gene060778:CDS
AGAGGGAGTGAAGTTGTGTC+TGG 0.393350 4.4:-70834319 None:intergenic
AAAGTAGAAGATTCTATGAT+TGG 0.404469 4.4:+70834404 MS.gene060778:CDS
TTCTTCAAGGCTACCTCATA+AGG 0.409509 4.4:-70834487 None:intergenic
CTTAGGTTTCTCCTCTGCAT+TGG 0.423443 4.4:-70833516 None:intergenic
CAAACTGTAGTGAGAGTTTG+AGG 0.431351 4.4:-70833369 None:intergenic
GGATTGAATAGTAGAATTTG+TGG 0.442017 4.4:-70833290 None:intergenic
AACAGGTTCATAATTCTTCA+AGG 0.442631 4.4:-70834500 None:intergenic
CCAAGACGATCAACCATGTC+TGG 0.451377 4.4:-70834523 None:intergenic
CGATCAACCATGTCTGGAAC+AGG 0.460674 4.4:-70834517 None:intergenic
TACATAAGTGATACAGCATA+TGG 0.462641 4.4:-70834617 None:intergenic
GATGATGAAGGTTGGATTGG+AGG 0.480496 4.4:+70833473 MS.gene060778:CDS
AATAGTAGAATTTGTGGAGA+AGG 0.498829 4.4:-70833284 None:intergenic
AAAATTAGAGGATCCTTATG+AGG 0.498846 4.4:+70834474 MS.gene060778:CDS
AATGATGATGAAGGTTGGAT+TGG 0.510553 4.4:+70833470 MS.gene060778:CDS
TGGATTCTTGTGTCAACTCC+AGG 0.515932 4.4:-70833440 None:intergenic
GGGAGAATGATGATGAAGGT+TGG 0.524754 4.4:+70833465 MS.gene060778:CDS
CTTCATCATCATTCTCCCAA+TGG 0.525735 4.4:-70833460 None:intergenic
GACTTGCAACTTCTTGAGCA+AGG 0.527830 4.4:-70834429 None:intergenic
GACATGGTTGATCGTCTTGG+TGG 0.530101 4.4:+70834526 MS.gene060778:CDS
CCAGACATGGTTGATCGTCT+TGG 0.532935 4.4:+70834523 MS.gene060778:CDS
AGTTGACACAAGAATCCATT+GGG 0.545872 4.4:+70833445 MS.gene060778:CDS
TTATGAACCTGTTCCAGACA+TGG 0.570153 4.4:+70834510 MS.gene060778:CDS
ACTTGCAACTTCTTGAGCAA+GGG 0.574767 4.4:-70834428 None:intergenic
ACATGGTTGATCGTCTTGGT+GGG 0.606623 4.4:+70834527 MS.gene060778:CDS
CATTGGGAGAATGATGATGA+AGG 0.623650 4.4:+70833461 MS.gene060778:CDS
AGCTTTCAGGAAACTATCAA+AGG 0.628834 4.4:+70834288 MS.gene060778:CDS
GAGTTGACACAAGAATCCAT+TGG 0.644255 4.4:+70833444 MS.gene060778:CDS
ACAGCAACAAACCAATGCAG+AGG 0.659212 4.4:+70833505 MS.gene060778:CDS
GCTTCTACTAAGGACACTCA+AGG 0.674014 4.4:+70833401 MS.gene060778:CDS
ATTCTTGTGTCAACTCCAGG+TGG 0.739348 4.4:-70833437 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GTTAAGATAAAAATATCAAA+GGG + chr4.4:70834002-70834021 MS.gene060778:intron 15.0%
!!! TAAGAAGAATAAGATTTTTT+AGG + chr4.4:70833336-70833355 MS.gene060778:CDS 15.0%
!!! TAGTTTAAAATTGAATTTCA+AGG - chr4.4:70833690-70833709 None:intergenic 15.0%
!! GAAACTGAAAATAAAATTAG+AGG + chr4.4:70834462-70834481 MS.gene060778:CDS 20.0%
!! GGTTAAGATAAAAATATCAA+AGG + chr4.4:70834001-70834020 MS.gene060778:intron 20.0%
!!! TAATTTCATGAATTTTTCTG+AGG - chr4.4:70834353-70834372 None:intergenic 20.0%
!!! TCTTATTCTTCTTATTGTTT+TGG - chr4.4:70833330-70833349 None:intergenic 20.0%
! AAAGTAGAAGATTCTATGAT+TGG + chr4.4:70834404-70834423 MS.gene060778:CDS 25.0%
! ACTAGAAGTTAGTATATGTT+TGG + chr4.4:70833706-70833725 MS.gene060778:intron 25.0%
!! CGATGGTTTTTATAAAATCA+CGG - chr4.4:70833821-70833840 None:intergenic 25.0%
!! GGCAAAATTTAGTTTACAAT+CGG - chr4.4:70833669-70833688 None:intergenic 25.0%
!! TGGTGTTTTATAGTTTTTGT+AGG - chr4.4:70833620-70833639 None:intergenic 25.0%
!! TTATTTTCAGTTTCTCTTGT+TGG - chr4.4:70834456-70834475 None:intergenic 25.0%
AAAATTAGAGGATCCTTATG+AGG + chr4.4:70834474-70834493 MS.gene060778:CDS 30.0%
AACAGGTTCATAATTCTTCA+AGG - chr4.4:70834503-70834522 None:intergenic 30.0%
AATAGTAGAATTTGTGGAGA+AGG - chr4.4:70833287-70833306 None:intergenic 30.0%
AGGCTAAAACAACTATTAGT+CGG + chr4.4:70833929-70833948 MS.gene060778:intron 30.0%
ATGAAAACAAGCAGATTCTT+AGG + chr4.4:70834229-70834248 MS.gene060778:intron 30.0%
CTACTATTCAATCCAATCTT+AGG + chr4.4:70833299-70833318 MS.gene060778:CDS 30.0%
GACATAATAGAAAATCGAAG+TGG - chr4.4:70833647-70833666 None:intergenic 30.0%
GGATTGAATAGTAGAATTTG+TGG - chr4.4:70833293-70833312 None:intergenic 30.0%
TACATAAGTGATACAGCATA+TGG - chr4.4:70834620-70834639 None:intergenic 30.0%
TCAGCTAAAGTTGAATAGTT+TGG + chr4.4:70833877-70833896 MS.gene060778:intron 30.0%
! AATTTTCACGTTGTTACGAA+AGG - chr4.4:70833796-70833815 None:intergenic 30.0%
! ACATAATCGGTACATGTTTT+GGG + chr4.4:70833980-70833999 MS.gene060778:intron 30.0%
! TAGAAAATCGAAGTGGTTTT+TGG - chr4.4:70833640-70833659 None:intergenic 30.0%
!! CTTTTTCATGAAACAATCTC+TGG - chr4.4:70834163-70834182 None:intergenic 30.0%
!!! TGTTTGGATTAGCTTTTACA+AGG + chr4.4:70833722-70833741 MS.gene060778:intron 30.0%
AAAAACCATCGCTAAACCAA+AGG + chr4.4:70833830-70833849 MS.gene060778:intron 35.0%
AAGCAATCAAAGTAGCTTTC+AGG + chr4.4:70834275-70834294 MS.gene060778:CDS 35.0%
AGCTTTCAGGAAACTATCAA+AGG + chr4.4:70834288-70834307 MS.gene060778:CDS 35.0%
AGTTGACACAAGAATCCATT+GGG + chr4.4:70833445-70833464 MS.gene060778:CDS 35.0%
ATGTCAGAGTTTGATCGAAA+AGG - chr4.4:70833964-70833983 None:intergenic 35.0%
CGATCAAACTCTGACATAAT+CGG + chr4.4:70833967-70833986 MS.gene060778:intron 35.0%
TACGACTTGAGTTCAATTGT+TGG + chr4.4:70833901-70833920 MS.gene060778:intron 35.0%
TGTTGAAATGACAAGAGTTG+CGG + chr4.4:70834189-70834208 MS.gene060778:intron 35.0%
! AATGATGATGAAGGTTGGAT+TGG + chr4.4:70833470-70833489 MS.gene060778:CDS 35.0%
! GACATAATCGGTACATGTTT+TGG + chr4.4:70833979-70833998 MS.gene060778:intron 35.0%
! GAGAAACCTAAGAAGCTTTT+GGG + chr4.4:70833527-70833546 MS.gene060778:CDS 35.0%
! GAGTTCAATTGTTGGCTAAA+AGG + chr4.4:70833909-70833928 MS.gene060778:intron 35.0%
! TTTCAGGATTTTCACGTCTA+CGG - chr4.4:70833761-70833780 None:intergenic 35.0%
!!! AAGGTTGCTTTTGTAGTTTC+AGG - chr4.4:70833777-70833796 None:intergenic 35.0%
!!! GCTGATTTGCTCAATTTTCA+AGG + chr4.4:70833560-70833579 MS.gene060778:CDS 35.0%
!!! GTTTTGGTGTTTCCTAAGAT+TGG - chr4.4:70833314-70833333 None:intergenic 35.0%
!!! TTTCTGAGGCTGTTTTTAGA+GGG - chr4.4:70834339-70834358 None:intergenic 35.0%
!!! TTTTCTGAGGCTGTTTTTAG+AGG - chr4.4:70834340-70834359 None:intergenic 35.0%
ACTTGCAACTTCTTGAGCAA+GGG - chr4.4:70834431-70834450 None:intergenic 40.0%
AGTTACACTTAGTGCTCCTT+TGG - chr4.4:70833849-70833868 None:intergenic 40.0%
ATTGCTTCTACATCAGCTTC+TGG - chr4.4:70834262-70834281 None:intergenic 40.0%
CAAACTGTAGTGAGAGTTTG+AGG - chr4.4:70833372-70833391 None:intergenic 40.0%
CTTCATCATCATTCTCCCAA+TGG - chr4.4:70833463-70833482 None:intergenic 40.0%
GAGTTGACACAAGAATCCAT+TGG + chr4.4:70833444-70833463 MS.gene060778:CDS 40.0%
GCAAGTTCATGCTTCTACTA+AGG + chr4.4:70833391-70833410 MS.gene060778:CDS 40.0%
TCTTCACCCAAAAGCTTCTT+AGG - chr4.4:70833536-70833555 None:intergenic 40.0%
TTATGAACCTGTTCCAGACA+TGG + chr4.4:70834510-70834529 MS.gene060778:CDS 40.0%
TTCTTCAAGGCTACCTCATA+AGG - chr4.4:70834490-70834509 None:intergenic 40.0%
! CATTGGGAGAATGATGATGA+AGG + chr4.4:70833461-70833480 MS.gene060778:CDS 40.0%
! GGAGAAACCTAAGAAGCTTT+TGG + chr4.4:70833526-70833545 MS.gene060778:CDS 40.0%
! TGACAAGAGTTGCGGATTAA+TGG + chr4.4:70834197-70834216 MS.gene060778:intron 40.0%
! TTCAGGATTTTCACGTCTAC+GGG - chr4.4:70833760-70833779 None:intergenic 40.0%
!! TGCATTGGTTTGTTGCTGTT+TGG - chr4.4:70833504-70833523 None:intergenic 40.0%
ACAGCAACAAACCAATGCAG+AGG + chr4.4:70833505-70833524 MS.gene060778:CDS 45.0%
ACATGGTTGATCGTCTTGGT+GGG + chr4.4:70834527-70834546 MS.gene060778:CDS 45.0%
ATTCTTGTGTCAACTCCAGG+TGG - chr4.4:70833440-70833459 None:intergenic 45.0%
CTTAGGTTTCTCCTCTGCAT+TGG - chr4.4:70833519-70833538 None:intergenic 45.0%
GACTTGCAACTTCTTGAGCA+AGG - chr4.4:70834432-70834451 None:intergenic 45.0%
GCTTCTACTAAGGACACTCA+AGG + chr4.4:70833401-70833420 MS.gene060778:CDS 45.0%
TGGATTCTTGTGTCAACTCC+AGG - chr4.4:70833443-70833462 None:intergenic 45.0%
! GATGATGAAGGTTGGATTGG+AGG + chr4.4:70833473-70833492 MS.gene060778:CDS 45.0%
! GGGAGAATGATGATGAAGGT+TGG + chr4.4:70833465-70833484 MS.gene060778:CDS 45.0%
AGAGGGAGTGAAGTTGTGTC+TGG - chr4.4:70834322-70834341 None:intergenic 50.0%
CCAAGACGATCAACCATGTC+TGG - chr4.4:70834526-70834545 None:intergenic 50.0%
CCAGACATGGTTGATCGTCT+TGG + chr4.4:70834523-70834542 MS.gene060778:CDS 50.0%
GACATGGTTGATCGTCTTGG+TGG + chr4.4:70834526-70834545 MS.gene060778:CDS 50.0%
! CGATCAACCATGTCTGGAAC+AGG - chr4.4:70834520-70834539 None:intergenic 50.0%
! GTGCTCCTTTGGTTTAGCGA+TGG - chr4.4:70833838-70833857 None:intergenic 50.0%
!! ACTCCAGGTGGTGCTTTTTG+TGG - chr4.4:70833428-70833447 None:intergenic 50.0%
!! GGACCACAAAAAGCACCACC+TGG + chr4.4:70833422-70833441 MS.gene060778:CDS 55.0%


Chromosome Type Strat End Strand Name
chr4.4 gene 70833266 70834660 70833266 ID=MS.gene060778
chr4.4 mRNA 70833266 70834660 70833266 ID=MS.gene060778.t1;Parent=MS.gene060778
chr4.4 exon 70833266 70833594 70833266 ID=MS.gene060778.t1.exon1;Parent=MS.gene060778.t1
chr4.4 CDS 70833266 70833594 70833266 ID=cds.MS.gene060778.t1;Parent=MS.gene060778.t1
chr4.4 exon 70834243 70834660 70834243 ID=MS.gene060778.t1.exon2;Parent=MS.gene060778.t1
chr4.4 CDS 70834243 70834660 70834243 ID=cds.MS.gene060778.t1;Parent=MS.gene060778.t1
Gene Sequence

>MS.gene060778

ATGGCTTCAACAGCAACACCTTCTCCACAAATTCTACTATTCAATCCAATCTTAGGAAACACCAAAACAATAAGAAGAATAAGATTTTTTAGGATAACAACAACCTCAAACTCTCACTACAGTTTGCAAGTTCATGCTTCTACTAAGGACACTCAAGGACCACAAAAAGCACCACCTGGAGTTGACACAAGAATCCATTGGGAGAATGATGATGAAGGTTGGATTGGAGGTAGCACCAAACAGCAACAAACCAATGCAGAGGAGAAACCTAAGAAGCTTTTGGGTGAAGATTTTGCTGATTTGCTCAATTTTCAAGGTTCTCATTATGAGTGAGTTTCTTTATAACTGTTTCCTACAAAAACTATAAAACACCAAAAACCACTTCGATTTTCTATTATGTCCGATTGTAAACTAAATTTTGCCTTGAAATTCAATTTTAAACTAGAAGTTAGTATATGTTTGGATTAGCTTTTACAAGGCAAATATCACGTCCCGTAGACGTGAAAATCCTGAAACTACAAAAGCAACCTTTCGTAACAACGTGAAAATTTACCGTGATTTTATAAAAACCATCGCTAAACCAAAGGAGCACTAAGTGTAACTAAAGCGTTTCAGCTAAAGTTGAATAGTTTGGATACGACTTGAGTTCAATTGTTGGCTAAAAGGCTAAAACAACTATTAGTCGGACTTTACTTCCTTTTCGATCAAACTCTGACATAATCGGTACATGTTTTGGGTTAAGATAAAAATATCAAAGGGTTTGTTGCATTGTGAACTCAAGTTTAGTCAAGATACTATTATTAAATTCTGTTTTTTCTTCAGTGAATATGAGAATTTTCTTTTTTTTTTTAAAAAAAAAAAAGAACAACTTGTGCATAAGTTGCTAACATACTACCAGAGATTGTTTCATGAAAAAGCTAGTTTGTTGAAATGACAAGAGTTGCGGATTAATGGATAACTATGATGAAAACAAGCAGATTCTTAGGAATATCACCAGAAGCTGATGTAGAAGCAATCAAAGTAGCTTTCAGGAAACTATCAAAGGAGTATCATCCAGACACAACTTCACTCCCTCTAAAAACAGCCTCAGAAAAATTCATGAAATTAAAAGAAGTTTACACTGTTCTGAGCAATGAAGAAAGTAGAAGATTCTATGATTGGACCCTTGCTCAAGAAGTTGCAAGTCGCCAACAAGAGAAACTGAAAATAAAATTAGAGGATCCTTATGAGGTAGCCTTGAAGAATTATGAACCTGTTCCAGACATGGTTGATCGTCTTGGTGGGAAGAATATGAAGCTTAGTGATCAAGCTGTTTCTGCTATCACTATTGATATTTTTATCATTATTTTTTCCATATGCTGTATCACTTATGTAGTTTTCTTTAAAGAATACTGA

Protein sequence

>MS.gene060778.t1

MASTATPSPQILLFNPILGNTKTIRRIRFFRITTTSNSHYSLQVHASTKDTQGPQKAPPGVDTRIHWENDDEGWIGGSTKQQQTNAEEKPKKLLGEDFADLLNFQGSHYEFLGISPEADVEAIKVAFRKLSKEYHPDTTSLPLKTASEKFMKLKEVYTVLSNEESRRFYDWTLAQEVASRQQEKLKIKLEDPYEVALKNYEPVPDMVDRLGGKNMKLSDQAVSAITIDIFIIIFSICCITYVVFFKEY